5VAD

Crystal structure of human Prolyl-tRNA synthetase (PRS) in complex with inhibitor

Summary for 5VAD

• Entry DOI: 10.2210/pdb5vad/pdb
• Descriptor: Bifunctional glutamate/proline--tRNA ligase, 3-[(cyclohexanecarbonyl)amino]-N-(2,3-dihydro-1H-inden-2-yl)pyrazine-2-carboxamide, PROLINE, ... (5 entities in total)
• Functional Keywords: aminoacyl-trna synthetase, atp dependent, inhibitor, ligase-ligase inhibitor complex, ligase/ligase inhibitor
• Biological source: Homo sapiens (Human)
• Cellular location: Cytoplasm : P07814
• Total number of polymer chains: 2
• Total formula weight: 117901.27

Authors

Okada, K.,Skene, R.J. (deposition date: 2017-03-24, release date: 2017-05-31, Last modification date: 2024-10-30)

Primary citation

Adachi, R.,Okada, K.,Skene, R.,Ogawa, K.,Miwa, M.,Tsuchinaga, K.,Ohkubo, S.,Henta, T.,Kawamoto, T.
Discovery of a novel prolyl-tRNA synthetase inhibitor and elucidation of its binding mode to the ATP site in complex with l-proline.
Biochem. Biophys. Res. Commun., 488:393-399, 2017

PubMed Abstract: Prolyl-tRNA synthetase (PRS) is a member of the aminoacyl-tRNA synthetase family of enzymes and catalyzes the synthesis of prolyl-tRNA using ATP, l-proline, and tRNA as substrates. An ATP-dependent PRS inhibitor, halofuginone, was shown to suppress autoimmune responses, suggesting that the inhibition of PRS is a potential therapeutic approach for inflammatory diseases. Although a few PRS inhibitors have been derivatized from natural sources or substrate mimetics, small-molecule human PRS inhibitors have not been reported. In this study, we discovered a novel series of pyrazinamide PRS inhibitors from a compound library using pre-transfer editing activity of human PRS enzyme. Steady-state biochemical analysis on the inhibitory mode revealed its distinctive characteristics of inhibition with proline uncompetition and ATP competition. The binding activity of a representative compound was time-dependently potentiated by the presence of l-proline with K of 0.76 nM. Thermal shift assays demonstrated the stabilization of PRS in complex with l-proline and pyrazinamide PRS inhibitors. The binding mode of the PRS inhibitor to the ATP site of PRS enzyme was elucidated using the ternary complex crystal structure with l-proline. The results demonstrated the different inhibitory and binding mode of pyrazinamide PRS inhibitors from preceding halofuginone. Furthermore, the PRS inhibitor inhibited intracellular protein synthesis via a different mode than halofuginone. In conclusion, we have identified a novel drug-like PRS inhibitor with a distinctive binding mode. This inhibitor was effective in a cellular context. Thus, the series of PRS inhibitors are considered to be applicable to further development with differentiation from preceding halofuginone.

PubMed: 28501621
DOI: 10.1016/j.bbrc.2017.05.064

Experimental method

X-RAY DIFFRACTION (2.36 Å)